Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate HSERO_RS02220 HSERO_RS02220 xylulokinase
Query= curated2:Q9X6C9 (495 letters) >FitnessBrowser__HerbieS:HSERO_RS02220 Length = 490 Score = 139 bits (349), Expect = 3e-37 Identities = 149/496 (30%), Positives = 223/496 (44%), Gaps = 56/496 (11%) Query: 5 LALDQGTTSSWAILFTLEGEVVAVAQRAFAQHYPEPGLVEHDPWEIWESQLWAAKEALRR 64 L +D GT+ A++ +G +VA+A P P E P + W++ A R Sbjct: 3 LGIDLGTSEVKAVVIDAQGSLVALAGSTLNVARPHPRWSEQAPADWWQATCDTV--AKLR 60 Query: 65 AGVGPE---AVLALGIANQRE-TTLVWERDTGRPLHPAIVWQDRRTASLCEALRERG--L 118 +G E ++ A+G++ Q L+ ERD L PAI+W D R+A C L R L Sbjct: 61 TQLGSERFGSIRAIGLSGQMHGAVLLDERD--EVLRPAILWSDSRSAPECAELESRAPRL 118 Query: 119 EGLFRARTGLLLDPYFSATKLLWLLERVPGLRERAERGEVCFGTV---DTWLLWNLTGGR 175 G+ G L P F+A KLLW+ P L R TV WL +TG + Sbjct: 119 HGI----AGNLAMPGFTAPKLLWVARHEPQLFAR-------IATVLLPKDWLRLKMTGRK 167 Query: 176 VHATDPTNASRTLLFHLETLTWDEELLRVLGIPKALLPEVRPSDGDFGETLPGL-----L 230 V +DP++A+ TL +E W +ELL G+ + +P + G LP + L Sbjct: 168 V--SDPSDAAGTLWLDVEGRNWSDELLAASGMRRDQMPALVDGSAVSGSLLPEVAQAWGL 225 Query: 231 GAPIPIRGVLGDQQAALLGQAALGAGEGKCTYGT-GAFLLLNTGERPVWAEG--GLLTTL 287 + + + G GD A+ +G A+ G+G + GT G ++N RP TL Sbjct: 226 RSDVIVAGGAGDGAASAVGIGAVKPGDGFLSLGTSGVLFVVNDRFRPNPGRAIHAFCHTL 285 Query: 288 A--WHLEGKAAYALEGSVFVAGAA-VGWLREVGLLGESH---EVESLARQVEDAGGVYFV 341 WH + SV ++ A+ + W + + E E+E L Q + + F+ Sbjct: 286 PQRWH---------QMSVMLSAASCLRWFCRLCSVDEKSLLAEIEQLDEQACNNAPL-FL 335 Query: 342 PAFTGLGAPHWDPYARGAILGLTRGTTRAHLARAALEGVAFSVGEVAWAMAGAAGLGLKA 401 P +G PH DPYA G GLT RA L A LEGVAF + + A+ AAG + Sbjct: 336 PYLSGERTPHNDPYATGVFHGLTPEHQRAALGYAVLEGVAFGMVDGLDALR-AAGTDVAE 394 Query: 402 LKADGGMAQNDLFLEIQADLLGVPVLRPRVTET-TALGAAWARGIGAGALSLGDLPALWR 460 L GG A++ + ++ AD L V ++ +E ALGAA + G GD + R Sbjct: 395 LSLVGGGARSAYWAQLLADALQVRIVTHVGSEAGGALGAARLAWLADG----GDEAEVCR 450 Query: 461 EEARFLPRMPEARREA 476 + A+ P+ R A Sbjct: 451 KPAQQALYQPDPARHA 466 Lambda K H 0.320 0.138 0.434 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 632 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 495 Length of database: 490 Length adjustment: 34 Effective length of query: 461 Effective length of database: 456 Effective search space: 210216 Effective search space used: 210216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory